The first five files concern data on 20 diallelic loci on 120
subjects. These data are
distributed with the Haploview package (Barrett et al., 2003). The
sixth files contains a additional dataset of 18 SNPs in
100 subjects, coded in "long" format, and the seventh file duplicates
this dataset in an alternative long format. These seven files are used
in the data input
vignette. The final file is a sample imputed genotype
dataset distributed with the MACH imputation package, and used in the
imputation vignette.
These files are stored in the extdata relative to the
package base. Full file names can be obtained using the
system.file function.
Format
The following files are described here:
sample.ped.gz: A gzipped pedfile
sample.info: An accompanying locus information file
sample.bed: The corresponding PLINK .bed file
sample.bim: The PLINK .bim file
sample.fam: The PLINK .fam file
sample-long.gz: A sample of long-formatted data
sample-long-alleles.gz: The same as above, but allele-coded
mach1.out.mlprob.gz: An mlprob output file from
the MACH genotype imputation program. This file contains, for each
imputed genotype call, posterior probabilities for the three possible
genotypes